CompaRNA - on-line benchmarks of RNA structure prediction methods

CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Table of contents:

Overview

Performance Plots

Performance of IPknot - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Multilign(seed) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for IPknot & Multilign(seed) [.zip] - may take several seconds...

Overview

Metric	IPknot		Multilign(seed)
MCC	0.560	>	0.538
Average MCC ± 95% Confidence Intervals	0.549 ± 0.276	>	0.478 ± 0.538
Sensitivity	0.435	>	0.420
Positive Predictive Value	0.732	>	0.699
Total TP	60	>	58
Total TN	11956	>	11955
Total FP	23	<	26
Total FP CONTRA	2	=	2
Total FP INCONS	20	<	23
Total FP COMP	1	=	1
Total FN	78	<	80
P-value	0.0

Performance plots

Performance of IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	60
Total TN	11956
Total FP	23
Total FP CONTRA	2
Total FP INCONS	20
Total FP COMP	1
Total FN	78

Total Scores
MCC	0.560
Average MCC ± 95% Confidence Intervals	0.549 ± 0.276
Sensitivity	0.435
Positive Predictive Value	0.732
Nr of predictions	4

2. Individual counts for IPknot [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.40	0.30	0.55	6	1529	5	1	4	0	14
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.61	0.48	0.80	20	3891	5	0	5	0	22
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28

Performance of Multilign(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for Multilign(seed)

Total Base Pair Counts
Total TP	58
Total TN	11955
Total FP	26
Total FP CONTRA	2
Total FP INCONS	23
Total FP COMP	1
Total FN	80

Total Scores
MCC	0.538
Average MCC ± 95% Confidence Intervals	0.478 ± 0.538
Sensitivity	0.420
Positive Predictive Value	0.699
Nr of predictions	4

2. Individual counts for Multilign(seed) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1528	12	1	11	0	20
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.55	0.45	0.68	19	3888	9	1	8	0	23
4AOB_A	SAM links to Rfam database...	0.61	0.45	0.83	19	4348	5	0	4	1	23

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.